fslmaths subtraction function gives error: output can't be found - unix

Question

the code will not create the output 'imdiff' but instead will say it can't find imdiff.
dyn896-105:intro sophiejacobs$ pwd
/Users/sophiejacobs/Downloads/preCourse/intro
dyn896-105:intro sophiejacobs$ ls
LThal_mask_func.nii.gz filtered_func_data.nii.gz
LThal_mask_std.nii.gz highres.nii.gz
bighead.nii.gz image0.nii.gz
bvals image1.nii.gz
cst2standard_73_46_26.nii.gz newfmri.nii.gz
diffdata.nii.gz standard.nii.gz
egepi.nii.gz structural.nii.gz
egfmri.nii.gz sub3m0.nii.gz
example_func.nii.gz thresh_zstat1.nii.gz
example_func2highres.mat wrapped.nii.gz
example_func2standard.mat
dyn896-105:intro sophiejacobs$ fslmaths image0 -sub image1 imdiff
libc++abi.dylib: terminating with uncaught exception of type `enter code here`NiftiIO::NiftiException: Error: cant open file imdiff.nii.gz
Abort trap: 6
I expected that image1 would be subtracted from image0 and that that new image would be called imdiff

Answer 1

I think I had the same error and came across your post when trying to fix it
NBrMBP:intro colette$ fslmaths image0 -sub image1 imdiff
libc++abi.dylib: terminating with uncaught exception of type NiftiException: Error: cant open file imdiff.nii.gz
Luckily my supervisor was able to help.
I did not have permission to the directory/folders/files that I downloaded from the FSL tutorial website, but worked after I changed the permissions
cd to the folder that has the files you are trying to use (for me this was a folder called preCourse)
use the command: ls –la
This lists details of the files in the directory. In the left hand column it shows the permissions with dr-xr-xr-x# which means I only had permission to read the files.
e.g:
`NBrMBP:preCourse colette$ ls -la
total 16
dr-xr-xr-x# 3 colette staff 102 21 Jul 2017 fmri
dr-xr-xr-x# 23 colette staff 782 21 Jul 2017 intro`
Use the command: chmod u+w <directoryname>
Run this from the folder above the one you would need permissions from. (u=user w = writing permissions)
e.g NBrMBP:preCourse colette$ chmod u+w intro
Now use ls –la again, it should now show drwxr-xr-x# in the left hand column i
e.g.:
NBrMBP:preCourse colette$ ls -la
total 16
drwx------# 5 colette staff 170 8 Jan 11:55 .
drwxr-xr-x 4 colette staff 136 8 Jan 11:55 ..
-rw-r--r--# 1 colette staff 6148 8 Jan 11:55 .DS_Store
drwxr-xr-x# 3 colette staff 102 21 Jul 2017 fmri
drwxr-xr-x# 26 colette staff 884 8 Jan 15:51 intro
*Note you may need admin permissions on your computer to be able to change the permissions of the read/write/executability of the files.
Hope this helps anyone else who searched the error code!